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- PDB-5fcb: Murine SMPDL3A in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 5fcb
TitleMurine SMPDL3A in complex with AMP
ComponentsAcid sphingomyelinase-like phosphodiesterase 3a
KeywordsHYDROLASE / SMPDL3A / sphingomyelin / nucleotide / AMP
Function / homology
Function and homology information


nucleoside triphosphate catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / negative regulation of cGAS/STING signaling pathway / nucleoside-triphosphate phosphatase / ATP hydrolysis activity / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Acid sphingomyelinase-like phosphodiesterase, predicted / Acid sphingomyelinase/endopolyphosphatase, metallophosphatase domain / Sphingomyelin phosphodiesterase, C-terminal domain / Acid sphingomyelin phosphodiesterase C-terminal region / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Cyclic GMP-AMP phosphodiesterase SMPDL3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsGorelik, A. / Illes, K. / Superti-Furga, G. / Nagar, B.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Nucleotide Hydrolysis by the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3A.
Authors: Gorelik, A. / Illes, K. / Superti-Furga, G. / Nagar, B.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acid sphingomyelinase-like phosphodiesterase 3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,81518
Polymers48,9971
Non-polymers3,81817
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.033, 132.381, 79.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-682-

HOH

21A-722-

HOH

31A-800-

HOH

41A-844-

HOH

51A-1105-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acid sphingomyelinase-like phosphodiesterase 3a / ASM-like phosphodiesterase 3a


Mass: 48997.258 Da / Num. of mol.: 1 / Fragment: UNP residues 23-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smpdl3a, Asml3a / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P70158, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Sugars , 3 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 525 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: citrate, PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.55→41.574 Å / Num. obs: 89133 / % possible obs: 93.7 % / Redundancy: 6.5 % / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.55→41.574 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 4414 4.96 %
Rwork0.1598 --
obs0.1611 88960 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→41.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 246 512 4147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073802
X-RAY DIFFRACTIONf_angle_d0.9255221
X-RAY DIFFRACTIONf_dihedral_angle_d11.9932271
X-RAY DIFFRACTIONf_chiral_restr0.053610
X-RAY DIFFRACTIONf_plane_restr0.007636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5496-1.56720.4417780.41281681X-RAY DIFFRACTION56
1.5672-1.58560.3584940.38311864X-RAY DIFFRACTION63
1.5856-1.6050.4058940.36252007X-RAY DIFFRACTION68
1.605-1.62530.39921080.34022211X-RAY DIFFRACTION73
1.6253-1.64670.30741170.31232327X-RAY DIFFRACTION79
1.6467-1.66920.30121390.28972506X-RAY DIFFRACTION84
1.6692-1.69310.32391400.27862681X-RAY DIFFRACTION89
1.6931-1.71840.27521550.26392818X-RAY DIFFRACTION95
1.7184-1.74520.2751490.24732957X-RAY DIFFRACTION98
1.7452-1.77380.28041490.23823001X-RAY DIFFRACTION100
1.7738-1.80440.24151680.22042973X-RAY DIFFRACTION100
1.8044-1.83720.24171480.212970X-RAY DIFFRACTION100
1.8372-1.87260.23691570.20532997X-RAY DIFFRACTION100
1.8726-1.91080.24911650.21093005X-RAY DIFFRACTION100
1.9108-1.95230.24191560.193001X-RAY DIFFRACTION100
1.9523-1.99770.2211600.16462980X-RAY DIFFRACTION100
1.9977-2.04770.18061540.16623025X-RAY DIFFRACTION100
2.0477-2.10310.20411610.16892988X-RAY DIFFRACTION100
2.1031-2.1650.17331550.15673022X-RAY DIFFRACTION100
2.165-2.23480.20641620.15612980X-RAY DIFFRACTION100
2.2348-2.31470.17971590.15243009X-RAY DIFFRACTION100
2.3147-2.40740.1511580.14143026X-RAY DIFFRACTION100
2.4074-2.51690.15771570.13863028X-RAY DIFFRACTION100
2.5169-2.64960.15561570.13683013X-RAY DIFFRACTION100
2.6496-2.81560.1561610.14373038X-RAY DIFFRACTION100
2.8156-3.03290.17841610.14473023X-RAY DIFFRACTION100
3.0329-3.3380.17681590.14243061X-RAY DIFFRACTION100
3.338-3.82070.16571620.13513047X-RAY DIFFRACTION100
3.8207-4.81250.13981650.11693107X-RAY DIFFRACTION100
4.8125-41.58930.18921660.15943200X-RAY DIFFRACTION100

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